Load prepared data
prepared_data <- read.table("../data/features.tsv", sep = "\t", header=TRUE)
totalTable <- NULL
totalTable$sd <- prepared_data$sd
totalTable$mean <- prepared_data$mean
totalTableOfMeans <- NULL
totalTableOfMeans$sd <- prepared_data$MeansSD
y <- NULL
y$Means <- prepared_data$res
ylog <- NULL
ylog$Means <- prepared_data$logres
Graphics of dependencies of result on different features
library(lattice)
xyplot(ylog$Means ~ prepared_data$Amplicon_GC_content, xlab="GC-content(%)", ylab="log of amplicon percental amount", main="Amplicon GC-content")
xyplot(ylog$Means ~ prepared_data$Amplicon_Len, xlab="Length", ylab="log of amplicon percental amount", main="Amplicon length")
xyplot(ylog$Means ~ prepared_data$Fwd_Primer_GC_content, xlab="GC-content(%)", ylab="log of amplicon percental amount", main="Forward Primer GC-content")
xyplot(ylog$Means ~ prepared_data$Fwd_Primer_Len, xlab="Length", ylab="log of amplicon percental amount", main="Forward Primer length")
xyplot(ylog$Means ~ prepared_data$Rev_Primer_GC_content, xlab="GC-content(%)", ylab="log of amplicon percental amount", main="Reverse Primer GC-content")
xyplot(ylog$Means ~ prepared_data$Rev_Primer_Len, xlab="Length", ylab="log of amplicon percental amount", main="Reverse Primer length")
xyplot(y$Means ~ prepared_data$Amplicon_GC_content, xlab="GC-content(%)", ylab="amplicon percental amount", main="Amplicon GC-content")
xyplot(y$Means ~ prepared_data$Amplicon_Len, xlab="Length", ylab="amplicon percental amount", main="Amplicon length")
xyplot(y$Means ~ prepared_data$Fwd_Primer_GC_content, xlab="GC-content(%)", ylab="amplicon percental amount", main="Forward Primer GC-content")
xyplot(y$Means ~ prepared_data$Fwd_Primer_Len, xlab="Length", ylab="amplicon percental amount", main="Forward Primer length")
xyplot(y$Means ~ prepared_data$Rev_Primer_GC_content, xlab="GC-content(%)", ylab="amplicon percental amount", main="Reverse Primer GC-content")
xyplot(y$Means ~ prepared_data$Rev_Primer_Len, xlab="Length", ylab="amplicon percental amount", main="Reverse Primer length")
xyplot(totalTable$mean ~ prepared_data$Amplicon_GC_content, xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Amplicon GC-content")
xyplot(totalTable$mean ~ prepared_data$Amplicon_Len, xlab="Length", ylab="mean of amplicon percental amount", main="Amplicon length")
xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_GC_content, xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Forward Primer GC-content")
xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_Len, xlab="Length", ylab="mean of amplicon percental amount", main="Forward Primer length")
xyplot(totalTable$mean ~ prepared_data$Rev_Primer_GC_content, xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Reverse Primer GC-content")
xyplot(totalTable$mean ~ prepared_data$Rev_Primer_Len, xlab="Length", ylab="mean of amplicon percental amount", main="Reverse Primer length")
xyplot(totalTable$sd ~ prepared_data$Amplicon_GC_content, xlab="GC-content(%)", ylab="sd of amplicon percental amount", main="Amplicon GC-content")
xyplot(totalTable$sd ~ prepared_data$Amplicon_Len, xlab="Length", ylab="sd of amplicon percental amount", main="Amplicon length")
xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_GC_content, xlab="GC-content(%)", ylab="sd of amplicon percental amount", main="Forward Primer GC-content")
xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_Len, xlab="Length", ylab="sd of amplicon percental amount", main="Forward Primer length")
xyplot(totalTable$sd ~ prepared_data$Rev_Primer_GC_content, xlab="GC-content(%)", ylab="sd of amplicon percental amount", main="Reverse Primer GC-content")
xyplot(totalTable$sd ~ prepared_data$Rev_Primer_Len, xlab="Length", ylab="sd of amplicon percental amount", main="Reverse Primer length")
xyplot(log(totalTable$mean) ~ prepared_data$Amplicon_GC_content, xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Amplicon GC-content")
xyplot(log(totalTable$mean) ~ prepared_data$Amplicon_Len, xlab="Length", ylab="mean of amplicon percental amount", main="Amplicon length")
xyplot(log(totalTable$mean) ~ prepared_data$Fwd_Primer_GC_content, xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Forward Primer GC-content")
xyplot(log(totalTable$mean) ~ prepared_data$Fwd_Primer_Len, xlab="Length", ylab="mean of amplicon percental amount", main="Forward Primer length")
xyplot(log(totalTable$mean) ~ prepared_data$Rev_Primer_GC_content, xlab="GC-content(%)", ylab="mean of amplicon percental amount", main="Reverse Primer GC-content")
xyplot(log(totalTable$mean) ~ prepared_data$Rev_Primer_Len, xlab="Length", ylab="mean of amplicon percental amount", main="Reverse Primer length")
xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_MaxPolyX, xlab="MaxPolyX", ylab="mean of amplicon percental amount", main="Forward Primer")
xyplot(totalTable$mean ~ prepared_data$Rev_Primer_MaxPolyX, xlab="MaxPolyX", ylab="mean of amplicon percental amount", main="Reverse Primer")
xyplot(totalTable$mean ~ prepared_data$Amplicon_MaxPolyX, xlab="MaxPolyX", ylab="mean of amplicon percental amount", main="Amplicon")
xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_MaxPolyX, xlab="MaxPolyX", ylab="sd of amplicon percental amount", main="Forward Primer")
xyplot(totalTable$sd ~ prepared_data$Rev_Primer_MaxPolyX, xlab="MaxPolyX", ylab="sd of amplicon percental amount", main="Reverse Primer")
xyplot(totalTable$sd ~ prepared_data$Amplicon_MaxPolyX, xlab="MaxPolyX", ylab="sd of amplicon percental amount", main="Amplicon")
xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_Entropy, xlab="Entropy", ylab="mean of amplicon percental amount", main="Forward Primer")
xyplot(totalTable$mean ~ prepared_data$Rev_Primer_Entropy, xlab="Entropy", ylab="mean of amplicon percental amount", main="Reverse Primer")
xyplot(totalTable$mean ~ prepared_data$Amplicon_Entropy, xlab="Entropy", ylab="mean of amplicon percental amount", main="Amplicon")
xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_Entropy, xlab="Entropy", ylab="sd of amplicon percental amount", main="Forward Primer")
xyplot(totalTable$sd ~ prepared_data$Rev_Primer_Entropy, xlab="Entropy", ylab="sd of amplicon percental amount", main="Reverse Primer")
xyplot(totalTable$sd ~ prepared_data$Amplicon_Entropy, xlab="Entropy", ylab="sd of amplicon percental amount", main="Amplicon")
xyplot(totalTable$mean ~ prepared_data$Fwd_Primer_Hash, xlab="Hash", ylab="mean of amplicon percental amount", main="Forward Primer")
xyplot(totalTable$mean ~ prepared_data$Rev_Primer_Hash, xlab="Hash", ylab="mean of amplicon percental amount", main="Reverse Primer")
xyplot(totalTable$mean ~ prepared_data$Amplicon_Hash, xlab="Hash", ylab="mean of amplicon percental amount", main="Amplicon")
xyplot(totalTable$sd ~ prepared_data$Fwd_Primer_Hash, xlab="Hash", ylab="sd of amplicon percental amount", main="Forward Primer")
xyplot(totalTable$sd ~ prepared_data$Rev_Primer_Hash, xlab="Hash", ylab="sd of amplicon percental amount", main="Reverse Primer")
xyplot(totalTable$sd ~ prepared_data$Amplicon_Hash, xlab="Hash", ylab="sd of amplicon percental amount", main="Amplicon")
Graphics of dependencies of standard variation of result
bwplot(prepared_data$Fwd_END_3 ~ ylog$Means, ylab="nucleotids", xlab="log of amplicon percental amount",
main="Forward primer 3' end")
bwplot(prepared_data$Rev_END_3 ~ ylog$Means, ylab="nucleotids", xlab="log of amplicon percental amount",
main="Reverse primer 3' end")
bwplot(prepared_data$Start_Dangling_End ~ ylog$Means, ylab="nucleotids", xlab="log of amplicon percental amount",
main="First dangling end")
bwplot(prepared_data$Stop_Dangling_End ~ ylog$Means, ylab="nucleotids", xlab="log of amplicon percental amount",
main="Second dangling end")
bwplot(prepared_data$Fwd_END_3 ~ y$Means, ylab="nucleotids", xlab="amplicon percental amount",
main="Forward primer 3' end")
bwplot(prepared_data$Rev_END_3 ~ y$Means, ylab="nucleotids", xlab="amplicon percental amount",
main="Reverse primer 3' end")
bwplot(prepared_data$Start_Dangling_End ~ y$Means, ylab="nucleotids", xlab="amplicon percental amount",
main="First dangling end")
bwplot(prepared_data$Stop_Dangling_End ~ y$Means, ylab="nucleotids", xlab="amplicon percental amount",
main="Second dangling end")
bwplot(prepared_data$Fwd_END_3 ~ totalTable$sd, ylab="nucleotids", xlab="standard deviation of amplicon percental amount",
main="Forward primer 3' end")
bwplot(prepared_data$Rev_END_3 ~ totalTable$sd, ylab="nucleotids", xlab="standard deviation of amplicon percental amount",
main="Reverse primer 3' end")
bwplot(prepared_data$Start_Dangling_End ~ totalTable$sd, ylab="nucleotids", xlab="standard deviation of amplicon percental amount",
main="First dangling end")
bwplot(prepared_data$Stop_Dangling_End ~ totalTable$sd, ylab="nucleotids", xlab="standard deviation of amplicon percental amount",
main="Second dangling end")
bwplot(prepared_data$Fwd_END_3 ~ totalTable$mean, ylab="nucleotids", xlab="mean of amplicon percental amount",
main="Forward primer 3' end")
bwplot(prepared_data$Rev_END_3 ~ totalTable$mean, ylab="nucleotids", xlab="mean of amplicon percental amount",
main="Reverse primer 3' end")
bwplot(prepared_data$Start_Dangling_End ~ totalTable$mean, ylab="nucleotids", xlab="mean of amplicon percental amount",
main="First dangling end")
bwplot(prepared_data$Stop_Dangling_End ~ totalTable$mean, ylab="nucleotids", xlab="mean of amplicon percental amount",
main="Second dangling end")
amplicon_len <- prepared_data$Amplicon_Len
q <- quantile(amplicon_len, probs = c(1/4, 1/2, 3/4, 1))
amplicon_len[amplicon_len <= q[1]] <- q[1]
amplicon_len[amplicon_len > q[1] & amplicon_len <= q[2]] <- q[2]
amplicon_len[amplicon_len > q[2] & amplicon_len <= q[3]] <- q[3]
amplicon_len[amplicon_len > q[3]] <- q[4]
histogram(amplicon_len)
bwplot(amplicon_len ~ y$Means, ylab="length", xlab="amplicon percental amount",
main="Amplicon length")
bwplot(amplicon_len ~ ylog$Means, ylab="length", xlab="log of amplicon percental amount",
main="Amplicon length")
bwplot(amplicon_len ~ totalTable$sd, ylab="length", xlab="standard deviation of amplicon percental amount",
main="Amplicon length")
bwplot(amplicon_len ~ totalTable$mean, ylab="length", xlab="mean of amplicon percental amount",
main="Amplicon length")
amplicon_gc <- prepared_data$Amplicon_GC_content
q <- quantile(amplicon_gc, probs = c(1/4, 1/2, 3/4, 1))
amplicon_gc[amplicon_gc <= q[1]] <- q[1]
amplicon_gc[amplicon_gc > q[1] & amplicon_gc <= q[2]] <- q[2]
amplicon_gc[amplicon_gc > q[2] & amplicon_gc <= q[3]] <- q[3]
amplicon_gc[amplicon_gc > q[3]] <- q[4]
histogram(amplicon_gc)
bwplot(amplicon_gc ~ y$Means, ylab="GC-content", xlab="amplicon percental amount",
main="Amplicon GC-content")
bwplot(amplicon_gc ~ ylog$Means, ylab="GC-content", xlab="log of amplicon percental amount",
main="Amplicon GC-content")
bwplot(amplicon_gc ~ totalTable$sd, ylab="GC-content", xlab="standard deviation of amplicon percental amount",
main="Amplicon GC-content")
bwplot(amplicon_gc ~ totalTable$mean, ylab="GC-content", xlab="mean of amplicon percental amount",
main="Amplicon GC-content")
primer_len <- prepared_data$Fwd_Primer_Len
q <- quantile(primer_len, probs = c(1/4, 1/2, 3/4, 1))
primer_len[primer_len <= q[1]] <- q[1]
primer_len[primer_len > q[1] & primer_len <= q[2]] <- q[2]
primer_len[primer_len > q[2] & primer_len <= q[3]] <- q[3]
primer_len[primer_len > q[3]] <- q[4]
histogram(primer_len)
bwplot(primer_len ~ y$Means, ylab="length", xlab="primer percental amount",
main="Forward Primer length")
bwplot(primer_len ~ ylog$Means, ylab="length", xlab="log of amplicon percental amount",
main="Forward Primer length")
bwplot(primer_len ~ totalTable$sd, ylab="length", xlab="standard deviation of amplicon percental amount",
main="Forward Primer length")
bwplot(primer_len ~ totalTable$mean, ylab="length", xlab="mean of amplicon percental amount",
main="Forward Primer length")
primer_gc <- prepared_data$Fwd_Primer_GC_content
q <- quantile(primer_gc, probs = c(1/4, 1/2, 3/4, 1))
primer_gc[primer_gc <= q[1]] <- q[1]
primer_gc[primer_gc > q[1] & primer_gc <= q[2]] <- q[2]
primer_gc[primer_gc > q[2] & primer_gc <= q[3]] <- q[3]
primer_gc[primer_gc > q[3]] <- q[4]
bwplot(primer_gc ~ y$Means, ylab="GC-content", xlab="primer percental amount",
main="Forward Primer GC-content")
bwplot(primer_gc ~ ylog$Means, ylab="GC-content", xlab="log of amplicon percental amount",
main="Forward Primer GC-content")
bwplot(primer_gc ~ totalTable$sd, ylab="GC-content", xlab="standard deviation of amplicon percental amount",
main="Forward Primer GC-content")
bwplot(primer_gc ~ totalTable$mean, ylab="GC-content", xlab="mean of amplicon percental amount",
main="Forward Primer GC-content")
primer_len <- prepared_data$Rev_Primer_Len
q <- quantile(primer_len, probs = c(1/4, 1/2, 3/4, 1))
primer_len[primer_len <= q[1]] <- q[1]
primer_len[primer_len > q[1] & primer_len <= q[2]] <- q[2]
primer_len[primer_len > q[2] & primer_len <= q[3]] <- q[3]
primer_len[primer_len > q[3]] <- q[4]
histogram(primer_len)
bwplot(primer_len ~ y$Means, ylab="length", xlab="primer percental amount",
main="Reverse Primer length")
bwplot(primer_len ~ ylog$Means, ylab="length", xlab="log of amplicon percental amount",
main="Reverse Primer length")
bwplot(primer_len ~ totalTable$sd, ylab="length", xlab="standard deviation of amplicon percental amount",
main="Reverse Primer length")
bwplot(primer_len ~ totalTable$mean, ylab="length", xlab="mean of amplicon percental amount",
main="Reverse Primer length")
primer_gc <- prepared_data$Rev_Primer_GC_content
q <- quantile(primer_gc, probs = c(1/4, 1/2, 3/4, 1))
primer_gc[primer_gc <= q[1]] <- q[1]
primer_gc[primer_gc > q[1] & primer_gc <= q[2]] <- q[2]
primer_gc[primer_gc > q[2] & primer_gc <= q[3]] <- q[3]
primer_gc[primer_gc > q[3]] <- q[4]
bwplot(primer_gc ~ y$Means, ylab="GC-content", xlab="primer percental amount",
main="Reverse Primer GC-content")
bwplot(primer_gc ~ ylog$Means, ylab="GC-content", xlab="log of amplicon percental amount",
main="Reverse Primer GC-content")
bwplot(primer_gc ~ totalTable$sd, ylab="GC-content", xlab="standard deviation of amplicon percental amount",
main="Reverse Primer GC-content")
bwplot(primer_gc ~ totalTable$mean, ylab="GC-content", xlab="mean of amplicon percental amount",
main="Reverse Primer GC-content")